Open /opt/php-5.4.12/etc/php-fpm.conf and adjust the following settings - in the listen line you must use an unused port (e.g. 8998; port 9000 might be in use by Debian's default PHP-FPM already), and you must add the line include=/opt/php-5.4.12/etc/pool.d/*.conf at the end:

In ISPConfig 3.0.5, you can configure the new PHP version under System > Additional PHP Versions. On the Name tab, you just fill in a name for the PHP version (e.g. PHP 5.4.12) - this PHP version will be listed under this name in the website settings in ISPConfig:

Go to the PHP-FPM Settings tab (the FastCGI Settings tab can be left empty) and fill out the fields as follows:

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I got errors when starting the init scripts for the FPM versions, and realized I had no var/run and var/log in my PHP directories under /opt, so I had to create them manually. Also, I tried 8999 and 8998, which I think were the ones it said to try if I remember correctly, but neither worked, it said ports not available. After some trial and error, I ended up using 8995 for 5.3.22 and 8991 for 5.4.12. I did not have these issues at all with the Ubuntu 13.04 version, although I've chosen to use Debian in the end because ISPConfig is a more solid setup there. I have yet to set these up within ISPConfig or install the FastCGI versions, but otherwise all is well despite those issues. Very helpful tutorial, thank you very much.